Ion traps according to Paul usually comprise a ring electrode and two end cap electrodes, the ring electrode usually being supplied with the storage RF voltage. Quadrupole filters with four pole rods according to Paul can also be used as ion traps. In this case diaphragms with ion-repelling potentials at both ends of the rod system are used to trap the ions inside the system. These so-called “linear quadrupole RF ion traps” are easier to fill with ions and can be filled with more ions than the “three-dimensional ion traps.” In the interior of the ion trap, ions can be stored in the quadrupole RF field. In a more general sense, ions also may be trapped in linear RF ion traps with more rods, such as hexapole or octopole rod systems, with apertured lens systems at both ends. In U.S. Pat. No. 5,572,035 (J. Franzen), lengthy ion guides made from stacked rings or from a double helix have been introduced. These ion guides can be used as linear RF ion traps, too. The designation “linear RF ion traps” shall here be used for all types of lengthy ion traps, whether rod systems like quadrupole, hexapole or octopole systems or whether such double helix or stacked ring systems.
With linear quadrupole RF ion traps, ions can be mass selectively ejected from these ion traps; the traps can thus being used as mass spectrometers. This is possible in two different ways—either radially through slits in one of the extended electrodes (U.S. Pat. No. 5,420,425, M. E. Bier and J. E. Syka, corresponding to EP 0 684 628 A1), or axially by means of coupling processes in the inhomogeneous end field of the rod system (“A new linear ion trap mass spectrometer”, J. W. Hager, Rapid Commun. Mass Spectrom. 2002, 16, 512–526). In both cases, one obtains a mass spectrometer if the ions mass selectively ejected are measured using a detection unit, for example a secondary-electron multiplier, and if the measurement data then are processed into a mass spectrum. The RF voltage on the four rods of the linear quadrupole mass spectrometer is usually high; for customary quadrupole mass spectrometers it is between 15 and 30 kilovolts (peak-to-peak). The frequency is around one megahertz. In the interior, a predominantly quadrupole field is created which oscillates with the RF voltage and drives the ions above a threshold mass to the center axis, causing these ions to execute so-called secular oscillations in this field.
Any linear ion trap is usually operated with a two-phase RF voltage, the two phases being applied alternately to the pole rods, to the helices, or to the rings in turn. An RF field is generated in the interior. On the axis of the linear trap system there is then no RF potential with respect to the ground potential of the mass spectrometer. The linear RF ion traps made from usual hexapole, octopole, double helix or stacked ring ion guides have usually much smaller inner diameters and do usually not need as high RF voltages as quadrupole systems used as mass spectrometers. Some hundred volts are sufficient with frequencies of some megahertz. These systems are simply operated by direct voltage output from MOSFET or similar devices, not using high gain transformers, exactly tuned to the capacity of the RF ion trap.
The RF voltage at the electrodes of the linear traps creates a widely inhomogeneous RF field inside the linear trap, effectively driving the ions back to the central axis of the trap, making the ions oscillate around or through the axis. A damping gas is regularly applied to damp the oscillations; the ions then gather in the axis of the linear RF ion trap. The restoring forces in the ion trap are sometimes described by a so-called pseudo-potential, which is determined by a temporal averaging of the forces of the real potential. For linear traps consisting of rods, there is a saddle point of the oscillating real potential in the center axis which decreases quadratically, depending on the phase of the RF voltage, from the saddle point down toward every second rod electrode, and increases quadratically up toward the other rod electrodes. The saddle point itself shows usually a DC potential with respect to the ground potential, as already described.
Quadrupole ion trap mass spectrometers have characteristics which make them of interest for many types of analyses. In particular, they can be used to isolate and fragment selected types of ion (so-called parent ions) in the ion trap. The spectra of these fragment ions are called “fragment ion spectra” or “daughter ion spectra” of the parent ions in question. It is also possible to measure “granddaughter ion spectra” as fragment ion spectra of selected daughter ions. Until now, the ions have been predominantly fragmented by a multitude of collisions with a collision gas, the oscillations of the ions to be fragmented being excited by an added dipole alternating field in such a way that the ions in the collisions can collect energy, a step which ultimately leads to the decay of the ions.
In other mass spectrometers using linear quadrupole systems, which are designed as so-called triple quadrupole mass spectrometers (“triple quads”), the daughter ions are generated by selecting the parent ions in an initial quadrupole mass filter and by fragmenting the parent ions to daughter ions by injecting them into a second quadrupole filter which is filled with collision gas; only then are they brought into the analyzing third linear quadrupole system.
The ions ultimately fragmented for the measurement of a daughter ion mass spectrum can be either generated in the interior of the linear ion trap or be introduced from outside. A collision gas in the linear ion trap ensures that the ion oscillations initially present are decelerated in the quadrupole RF field; the ions then collect as a small cloud on the center axis of the ion trap. The diameter of the string-shaped ion cloud in normal linear ion traps is around half a millimeter; it is determined by an equilibrium between the centering effect of the RF field (the restoring force of the pseudo-potential) and the repulsive coulomb forces between the ions. The internal dimensions of the RF ion trap are usually characterized by a separation of opposing rods of between three and twelve millimeters approximately.
A popular type of ionization of large biomolecules is the electrospray method (ESI=electro spray ionization), which ionizes ions at atmospheric pressure outside the mass spectrometer. These ions are then brought via inlet systems of a known type into the vacuum of the mass spectrometer and from there, mostly using intermediate RF ion guides, into a mass spectrometer.
This type of ionization generates practically no fragment ions, the ions being essentially those of the molecule. With electrosprays, multiply charged ions of the molecules do frequently occur, however. As a result of the lack of almost any fragment ion during the ionization process, the information from the mass spectrum is limited to the molecular weight; there is no information about internal molecular structures which can be used for the further identification of the substances present. This information can only be obtained by scanning fragment ion spectra (daughter ion spectra).
Recently, a method for the fragmentation of biomolecules, mainly peptides and proteins, has been developed for use in ion cyclotron resonance mass spectrometry (ICR-MS), also called Fourier transform mass spectrometry (FTMS). Low energy electrons are captured by multiply charged ions, whereby the ionization energy released leads to the fragmentation of the usually chain-shaped molecules. The method has become known as ECD (electron capture dissociation). If the molecules were doubly charged, one of the two fragments created remains as an ion. In this process, the fragmentation follows extremely simple rules (for specialists: there are predominantly c-cleavages and only a few a-cleavages and z-cleavages between the amino acids of a peptide), so that it is very simple to elucidate the structure of the molecule from the fragmentation pattern. In particular, the sequence of amino acids in the peptides or proteins is easy to read from the fragmentation spectrum. The interpretation of these ECD fragment spectra is much simpler than the interpretation of collisionally induced dissociation (CID) spectra.
It is also possible to fragment triply or multiply charged ions in this way, but the method really shines in the case of doubly charged ions. If an electrospray ionization is applied to peptides, the doubly charged ions are also the most prevalent ions, as a rule. Electrospray ionization is a method of ionization which is particularly frequently used for mass spectrometric analysis of biomolecules in RF ion traps and other types of mass spectrometers.
For fragmentation by electron capture, the kinetic energy of the electrons must be very low, below 3 eV, since otherwise there can be no capture. In most cases, one just offers electrons with an energy which lies just above the thermal energy of the electrons. Electrons with about 3 to 30 electron Volts can also be used, they generate “hot ECD” fragment ions. In the extremely strong magnetic fields of Fourier transform mass spectrometers this is very successful, because the electrons simply drift along the magnetic field lines until they reach the cloud of ions.